HIV-1, HIV-2, and SIV pol nucleotide fragments

ABSTRACT

The invention relates to polypeptide fragments of HIV-1, HIV-2, and SIV, antibodies that bind to the polypeptides of the invention, methods of using the antibodies, and kits containing the antibodies. The invention also relates to polynucleotides that encode the polypeptide fragments of the invention.

This is a divisional of application Ser. No. 08/472,928, filed Jun. 7,1995 (now U.S. Pat. No. 7,078,516); which is a divisional of applicationSer. No. 08/160,465, filed Dec. 2, 1993 (now U.S. Pat. No. 5,688,637);which is a continuation of application Ser. No. 07/820,599, which has a35 U.S.C. §371(c) date of Jan. 21, 1992 (now abandoned) and is anational stage application of International Application No.PCT/FR90/00393, filed Jun. 5, 1990, which claims priority to FrenchApplication No. 8907354, filed on Jun 2, 1989, and French ApplicationNo. 8912371, filed on Sep. 20, 1989.

The present invention relates to oligonucleotide sequences which can beused for the implementation of techniques for the amplification ofspecific nucleotide sequences of human immunodeficiency retroviruses ofthe HIV type or of monkey immunodeficiency retroviruses of the SIV type.

The invention relates in particular to the use of such sequences formethods of in vitro diagnosis in man of the infection of an individualby a retrovirus of the HIV type (at present HIV-1 and/or HIV-2).

The isolation and characterization of retroviruses grouped togetherunder the designations HIV-1 and HIV-2 were described in the Europeanpatent applications No. 85/905.513.9 and No. 87/400.151.4, respectively.These retroviruses were isolated from several patients exhibitingsymptoms of a lymphadenopathy or an Acquired Immunodeficiency Syndrome(AIDS).

The retroviruses of the HIV-2 type like the retroviruses of the HIV-1type are characterized by a tropism for the human T4 lymphocytes and bya cytopathogenic effect with regard to these lymphocytes when theymultiply within them to give rise to, among other things, generalizedand persistent polyadenopathies, or an AIDS.

Another retrovirus, designated SIV-1, this designation replacing theearlier one STLV-III, was isolated from the rhesus macaque monkey (M. D.DANIEL et al. Science, 228, 1201 (1985); N. L. LETWIN et al., Science,230, 71 (1985) under the designation “STLV-IIImac”).

Another retrovirus, designated “STLV-III_(AGM)” (or SIV_(AGM)), wasisolated from wild green monkeys. However, in contrast to the virusespresent in the rhesus macaque monkey, the presence of STLV-III_(AGM)does not appear to induce a disease of the AIDS type in the Africangreen monkey.

For reasons of semantics, these viruses will be designated in whatfollows only by the expression SIV (the expression SIV is an Englishabbreviation for “Simian Immunodeficiency Virus”, possibly followed byan abbreviation designating the species of monkey from which they arederived, for example “MAC” for “macaque” or “AGM” for the “African GreenMonkey”.

A strain of the retrovirus SIV-1Mac was deposited with the C.N.C.M. on 7February 1986 under the No. I-521.

The continuation of the study of the retroviruses HIV-1 and HIV-2 hasalso led to the production of DNA sequences (cDNA) complementary to theRNAs of their genome. The complete nucleotide sequence of a cDNA of aretrovirus representative of the HIV-2 class (HIV-2 ROD) was depositedon Feb. 21, 1986 with the C.N.C.M. under the No. I-522, under thereference name LAV-2 ROD.

Similarly, the complete nucleotide sequence of a cDNA of a retrovirusrepresentative of the HIV-1 class is described by WAIN-HOBSON, SONIGO,COLE, DANOS and ALIZON in CEll (January 1985).

Also for semantic reasons, the viruses of the HIV-1 and HIV-2 type willsometimes be designated in the subsequent description by the expressionHIV.

The methods for the in vitro diagnosis of the infections by viruses ofthe HIV-1 or HIV-2 type currently practised, are based on the detectionof anti-HIV-1 or anti-HIV-2 antibodies possibly present in a biologicalsample (biopsy) or in a biological fluid, for example in a serumobtained from the patient under study, by placing this biological fluidin contact with extracts or antigens of HIV-1 or HIV-2 under conditionswhich could give rise to the production of an immunological reactionbetween these extracts or antigens and these antibodies.

There is the risk that such diagnostic methods will give rise to falsenegatives, in particular in the case of a recent infection of anindividual by the viruses of the HIV type.

The techniques of gene amplification make a considerable contribution tothe development of in vitro diagnostic methods which are particularlysensitive for viral diseases. Among these techniques of geneamplification, mention may be made of the PCR (Polymerase ChainReaction) technique as described in the European patent applications No.86/302.298.4 of Mar. 27, 1986 and No. 87/300.203.4 of Sep. 1, 1987, oralso the technique known as “Qβreplicase” described in Biotechnology,vol. 6 page 1197 (October 1988) and that which makes use of a RNApolymerase (T7RNA polymerase) described in the International patentapplication No. WO89/01050. These techniques make it possible to improvethe sensitivity of detection of the nucleic acids of the virus, andrequire the use of specific primers for synthesis.

In the case of research on the viruses of the HIV type, the choice ofprimers is problematical. In fact, owing to the great variability of thenucleotide sequences of the viral genome, a primer corresponding to theknown sequence of a given isolate of a virus of the HIV type may fail inthe amplification of certain viral variants of the HIV type.Furthermore, even if a primer is selected from a region of the genomewhich is conserved from one HIV virus to another, its “efficiency” isnot thereby insured and may give rise to poor amplification yields.

The precise objective of the present invention is to provideoligonucleotide primers which, inter alia, make possible theamplification of the genome of all viruses of the HIV and SIV types, inparticular for diagnostic purposes, with yields considered to be maximalin the present state of the art and which, in particular, do not giverise to the presence of many aspecific bands.

The primers of the present invention are specific both for the virusesof the HIV-1 groups and/or the viruses of the HIV-2 and SIV groups, andare insensitive to variations of the genome of these viruses.

The object of the present invention is oligonucleotide primers of about15 to 30 nucleotides which can be used for the genomic amplification ofthe viruses of the HIV-I type and/or HIV-2 and SIV types.

The invention relates to any nucleotide sequence characterized in thatits sequence:

-   -   is either selected from those which are contained in one of the        nucleotide sequences included in the gag, vpr and pol genes of        the viruses HIV-1 Bru, HIV-1 Mal, HIV-1 Eli, HIV-2 ROD and SIV        MAC, or in the nef2, vif2 and vpx genes of the viruses HIV-2 ROD        and SIV MAC, or in the env, nef1, vif1 and vpr genes of the        viruses HIV-1 Bru, HIV-1 Mal and HIV-1 Eli, and more        particularly from those which are contained in the nucleotide        sequences defined hereafter,    -   or (particularly in the case of the longest sequences) contains        one of the above-mentioned nucleotide sequences derived from        HIV-1 Bru or HIV-1 Mal, or HIV-1 Eli or HIV-2 ROD or SIVMac, or        contains a complementary nucleotide sequence of one of these        latter sequences, it being understood that the possible        additional nucleotides which “extend beyond” the nucleotide        sequence of the type in question at the 3′ or 5′ ends preferably        coincide with those which are placed external to the 5′ or 3′        end of the same sequence within the complete sequence of the        viruses of the HIV-1, HIV-2 or SIV MAC type mentioned above,    -   or, if this nucleotide sequence is not identical with one of the        above-mentioned nucleotide sequences, or is not complementary to        one of these sequences, it is nonetheless capable of hybridizing        with a nucleotide sequence derived from the viruses HIV-1 Bru,        HIV-1 Mal, HIV-1 Eli and/or with a nucleotide sequence derived        from the viruses HIV-2 ROD or SIV MAC mentioned above. The        hybridization may be carried out at a temperature of 60°        C.±1° C. (preferably 60° C.±0.5° C.), recommended for an optimal        yield.

The numbering of the nucleotides mentioned below corresponds to thatused in the reference manual “Human Retrovirus and AIDS-1989” edited bythe “Los Alamos National Laboratory-New Mexico-USA”.

(The sequences of the viruses HIV-1 Mal, HIV-1 Eli were described byMONTAGNIER, SONIGO, WAIN-HOBSON and ALIZON in the European patentapplication No. 86.401380 of Jun. 23, 1986).

The sequences of the invention are synthesized in a synthesizer marketedby Applied Biosystems (phosphoro-amidite method) or in any otherapparatus employing a similar method.

The invention relates more particularly to the oligonucleotide sequencescharacterized by the following nucleotide sequences (shown in the 5′→3′sense; the initials “S” and “AS” indicate whether the oligonucleotide issense or anti-sense, i.e. whether the oligonucleotide is oriented in the5′→3′ or in the 3′→5′ sense):

-   1°) sequences common to the genomes of the HIV-1, HIV-2 and SIV    viruses (the pairs of numbers separated by a dash indicate the    position of the nucleotides in the genomes corresponding    respectively to the viruses HIV-1 Bru, HIV-1 Mal, HIV-1 Eli, HIV-2    ROD and SIV):    -   specific sequences of the gag gene of the genome of the        above-mentioned viruses (gene coding for a group of antigens        specific for the nucleoid of these viruses).

Certain variants may be introduced by certain positions of thenucleotide sequences indicated below, without affecting thehybridization properties of these nucleotide sequences with the genes ofthe viruses of the HIV and/or SIV types. The nucleotide sequencescontaining these variants are shown below the original nucleotidesequences from which they are derived by substitution of one or morebases. The bases representing modifications of the initial nucleotidesequences are indicated by a letter directly beneath the base which theyreplace in the initial sequences; whereas the bases of the originalsequences which are not replaced in the sequences bearing these variantsare shown by dots.

The synthesis of the primers is carried out by using all of the variantssimultaneously. It is the mixture of all of the variants for a givensequence which is used in the tests.

(SEQ ID NO: 1) MMy1: TGG CGC CCG AAC AGG GAC (SEQ ID NO: 2) ... ... ....T. ... ... S, 636-653, 635-652, 636-653, 859-876, 834-851 (SEQ ID NO:3) MMy2: GGC CAG GGG GAA AGA AAA A (SEQ ID NO: 4) ... .C. .C. ... ...... . (SEQ ID NO: 5) ... ... .A. ... ... ... . S, 854-872, 864-888,848-872, 1160-1184, 1124-1148 (SEQ ID NO: 6) MMy3: TGC CCA TAC AAA ATGTTT TA (SEQ ID NO: 7) ... ... C.. T.T ... ... .. AS, 900-881, 916,897,900-881, 1212-1193, 1176-1157 (SEQ ID NO: 8) MMy4: TGC ATG GCT GCT TGATG (SEQ ID NO: 9) ... ..A ... ..C ..G .. AS, 1385-1369, 1419-1403,1385-1369, 1703-1687, 1667-1651 (SEQ ID NO: 10) MMy4B: CTT TGC ATG GCTGCT TGA TG (SEQ ID NO: 11) ..C ... ..A ... ..C ..G .. AS, 1388-1369,1421-1403, 1388-1369, 1706-1687, 1670-1651 (SEQ ID NO: 12) MMy4Ba: CATCAA GCA GCC ATG CAA AG (SEQ ID NO: 13) ..C ..G ... ..T ... ..G .. S,1369-1388, 1403-1421, 1369-1388, 1687-1706, 1651-1670, (SEQ ID NO: 14)MMy28: AGG GCT GTT GGA AAT GTG G (SEQ ID NO: 15) ... ... ... ... ..G .... S, 2021-2039, 2055-2073, 2024-2042, 2329-2349, 2299-2318, (SEQ ID NO:16) MMy28a: CCA CAT TTC CAG CAT CCC T (SEQ ID NO: 17) ... ... ... .....G ... . (SEQ ID NO: 18) ... ... ... ... ..C ... . AS, 2039-2021,2073-2055, 2042-2024, 2349-2329, 2318-2299

(SEQ ID NO: 19) MMy18: GAT AGA TGG AAC AAG CCC CAG S, 5590-5610,5585-5605, 5554-5574, 6233-6296, 6147-6170 (SEQ ID NO: 20) MMY19: TCCATT TCT TGC TCT CCT CTG T AS, 5870-5849, 5865-5844, 5834-5813,6551-6531, 6454-6431,

-   -   specific sequence of the pol gene:

(SEQ ID NO: 21) MMy29: TAA AGC CAG GAA TGG ATG GCC CAA (SEQ ID NO: 22)... ... ... ... ... ... .A. ... S, 2620-2643, 2615-2638, 2584-2607,2971-2994, 2887-3010 (SEQ ID NO: 23) MMy29a: TTG GGC CAT CCA TTC CTG GCTTTA (SEQ ID NO: 24) ... .T. ... ... ... ... ... ... AS, 2643-2620,2638-2615, 2607-2584, 2994-2971, 3010-2887, (SEQ ID NO: 25) MMy30: TGGACT GTC AAT GAC ATA CAG AA (SEQ ID NO: 26) ... ... ... ... ..T ... ..... S, 3339-3361, 3334-3356, 3303-3325, 3690-3712, 3606-3628, (SEQ ID NO:27) MMy30a: TTC TGT ATG TCA TTG ACA GTC CA (SEQ ID NO: 28) ... ... ...... ... ..T ... .. AS, 3361-3339, 3356-3334, 3325-3303, 3712-3690,3628-3606, (SEQ ID NO: 29) MMy31: CAT GGG TAC CAG CAC ACA AAG G S,4186-4207, 4181-4202, 4150-4171, 4534-4555, 4450-4471, (SEQ ID NO: 30)MMy31a: CCT TTG TGT GCT GGT ACC CAT G AS, 4207-4186, 4202-4181,4171-4150, 4555-4534, 4471-4450, (SEQ ID NO: 31) MMy32: TGG AAA GGT GAAGGG GCA GT (SEQ ID NO: 32) ... ... ... ... ..A ... .. S, 4992-5011,4987-5006, 4956-4975, 5340-5359, 5256-5275, (SEQ ID NO: 33) MMy32: ACTGCC CCT TCA CCT TTC CA (SEQ ID NO: 34) ... ... ... ..T ... ... .. (SEQID NO: 35) ... ... ... ..C ... ... .. AS, 5011-4992, 5006-4987,4975-4956, 5359-5340, 5275-5256

-   2°) sequences common to the genomes of the HIV-2 and SIV viruses    (the pairs of numbers separated by a dash indicate the position of    the nucleotides in the genomes corresponding to the viruses HIV-2    ROD and SIV-MAC, respectively).    -   specific sequences of the nef2 gene        (coding for a negative factor of 27 kD)

(SEQ ID NO: 36) MMy12: AGA GAC TCT TGC GGG CGC GTG S, 9165-9185,9139-9159, (SEQ ID NO: 37) MMy13: ATA TAC TTA GAA AAG GAA GAA GG S,9542-9564, 9516-9538, (SEQ ID NO: 38) MMy13bis: CCT TCT TCC TTT TCT AAGTAT AT AS, 9564-9542, 9538-9516, (SEQ ID NO: 39) MMy14: AGC TGA GAC AGCAGG GAC TTT CCA AS, 9956-9933, 9893-9870,

-   -   specific sequences of vif2 gene (coding for an infectivity        factor of 23 kD)

(SEQ ID NO: 40) MMy20: TAT GGA GGA GGA AAA GAG ATG GAT AGT S, 5424-5450,5340-5366, (SEQ ID NO: 41) MMy21: TAG CAC TTA TTT CCC TTG CTT T S,5754-5775, 5670-5691, (SEQ ID NO: 42) MMy21bis: AAA GCA AGG GAA ATA AGTGCT A AS, 5775-5754, 5691-5670, (SEQ ID NO: 43) MMy22: CCC TTG TTC ATCATG CCA GTA T AS, 6082-6061, 5995-5974,

-   -   specific sequences of the vpx gene (coding for a protine of 12        kD)

(SEQ ID NO: 44) MMy23: ATG TCA GAT CCC AGG GAG A S, 5900-5918,5813-5831, (SEQ ID NO: 45) MMy24: CCT GGA GGG GGA GGA GGA GGA AS,6228-6208, 6141-6121,

-   3°) Sequences common to the genomes of the viruses HIV-1 Bru, HIV-1    Mal and HIV-1 Eli (the pairs of numbers separated by a dash indicate    the position of the nucleotides in the genomes corresponding to the    viruses HIV-1 Bru, HIV-1 Mal and HIV-1 Eli, respectively).    -   specific sequences of the env gene (coding for the envelope        proteins)

(SEQ ID NO: 46) MMy5: CCA ATT CCC ATA CAT TAT TGT GCC CC S, 6905-6930,6903-6928, 6860-6885 (SEQ ID NO: 47) MMy5: GGG GCA CAA TAA TGT ATG GGAATT GG AS, 6930-6905, 6928-6903, 6885-6860, (SEQ ID NO: 48) MMy6: AATGGC AGT CTA GCA GAA GAA GA S, 7055-7077, 7053-7075, 7010-7032 (SEQ IDNO: 49) MMy7: ATC CTC AGG AGG GGA CCC AGA AAT T S, 7360-7384, 7349-7373,7306-7330 (SEQ ID NO: 50) MMy7a: AAT TTC TGG GTC CCC TCC TGA GGA T AS,7384-7360, 7373-7349, 7330-7306 (SEQ ID NO: 51) MMy8: GTG CTT CCT GCTGCT CCC AAG AAC CC AS, 7857-7832, 7846-7821, 7800-7775 (SEQ ID NO: 52)MMy8a: GGG TTC TTG GGA GCA GCA GGA AGC AC S, 7832-7857, 7821-7846,7775-7800, (SEQ ID NO: 53) MMy9: ATG GGT GGC AAG TGG TCA AAA AGT AG (SEQID NO: 68) ... ... ... ..A ... ... ... ... .. S, 8877-8869, 8836-8861,8787-8812, (SEQ ID NO: 54) MMy9a: CTA CTT TTT GAC CAC TTG CCA CCC AT AS,8869-8844, 8861-8836, 8812-8787, (SEQ ID NO: 55) MMy78: TAT TAA CAA GAGATG GTG G S, 7629-7647, 7612-7630, 7572-7590, (SEQ ID NO: 56) MMy89: CCAGCA AGA AAA GAA TGA A S, 8224-8242, 8213-8231, 8167-8185, (SEQ ID NO:57) MMy89a: TTC ATT CTT TTC TTG CTG G AS, 8242-8224, 8231-8213,8185-8167,

-   -   specific sequences of the nef 1 gene:

(SEQ ID NO: 58) MMy10: AAA AGA AAA GGG GGG ACT GGA S, 9116-9136,9117-9137, 9062-9082, (SEQ ID NO: 59) MMy10a: TCC AGT CCC CCC TTT TCTTTT AS, 9136-9116, 9137-9117, 9082-9062, (SEQ ID NO: 60) MMy11: AAA GTCCCC AGC GGA AAG TCC C AS, 9503-9483, 9505-9484, 9449-9428,

-   -   specific sequences of the vif 1 gene

(SEQ ID NO: 61) MMy15: GAT TAT GGA AAA CAG ATG GCA GGT GAT S, 5073-5099,5068-5094, 5037-5063, (SEQ ID NO: 62) MMy16: GCA GAC CAA CTA ATT CAT CTGTA S, 5383-5405, 5378-5400, 5347-5369, (SEQ ID NO: 63) MMy16a: TAC AGATGA ATT AGT TGG TCT GC AS, 5405-5383, 5400-5378, 5369-5347, (SEQ ID NO:64) MMy17: CTT AAG CTC CTC TAA AAG CTC TA AS, 5675-5653, 5670-5648,5639-5617,

-   -   specific sequences of the vpu gene

(SEQ ID NO: 65) MMy25: GTA AGT AGT ACA TGT AAT GCA ACC T S, 6081-6105,6076-6100, 6045-6069, (SEQ ID NO: 66) MMy26: AGC AGA AGA CAG TGG CCA TGAGAG S, 6240-6263, 6238-6261, 6207-6230, (SEQ ID NO: 67) MMy27: ACT ACAGAT CAT ACC TAT CCC AA S, 6343-6321, 6338-6316, 6307-6285,

The object of the invention is also the sequences (or primers)possessing a complementary nucleotide structure to those of the primersdefined above.

It also relates to the nucleotide sequences possessing certain mutationswith respect to those defined above without the hybridizationproperties, such as defined above, of these sequences being modified.The percentage of nucleotides different from those constituting thesequences described above without thereby affecting the hybridizationproperties of the sequences of the invention may attain 40%.

Generally speaking, in the case of a sense (S) primer, a larger numberof mutations is tolerated at the 5′ end than at the 3′ end of theprimer, the 3′ end being required to hybridize perfectly with a specificstrand of a nucleotide sequence in order for this sequence to beamplified. In the case of an anti-sense (AS) primer, it is at the 3′ endthat tolerance is allowed.

The object of the invention is also the primers such as those definedabove and including a conserved stretch of at least 5 bases on eitherside of the central part which contains modifications without the abovehybridization properties being modified.

One of the characteristics of the oligonucleotide primers of theinvention is that of giving a clear-cut amplification band, usually freeof aspecific bands when the technical directions for use described inthe present invention are followed. This fact is due to the length ofthe primers which may attain 27 bases and thus increases the specificityof hybridization, as well as to the drastic conditions of use which makeit possible to eliminate parasitic combinations. In addition to thepercentage of homology with the reference matrix, the specificity foreach type of virus is a function of the length of the primer which mayattain as many as 40 bases in order to obtain an acceptable yield.

The invention also includes primers such as those described above linkedat their 5′ end to a promoter for the implementation of a method ofgenomic amplification by the synthesis of multiple copies of DNA or RNAsuch as that described in the European patent application No.88/307.102.9 of Jan. 8, 1988.

The object of the invention is in particular the use of the primersdescribed above for the implementation of a procedure of geneamplification of nucleotide sequences of the viruses of the HIV-1 and/orHIV-2 and/or SIV type, this procedure being applicable to the in vitrodiagnosis of the potential infection of an individual by a virus of theHIV-1 and/or HIV-2 type or of an animal by at least one of the threeviruses (HIV-1, HIV-2, SIV).

This method of in vitro diagnosis of the invention is carried outstarting from a biological sample (for example a biological fluid suchas serum, the lymphocytes of circulating blood) obtained from a patientunder study, and comprising mainly the following steps:

-   -   a step involving the extraction of the nucleic acid to be        detected belonging to the genome of the virus of the HIV-1        and/or HIV-2 and/or SIV type possibly present in the        above-mentioned biological sample and, where appropriate, a step        involving the incubation of the said nucleic acid with a reverse        transcriptase if this latter is in the form of RNA in order to        obtain a double-stranded nucleic acid (this last step being also        designated below as the step of retrotranscription of the viral        RNA),    -   a cycle comprising the following steps:        -   denaturation of the double-stranded nucleic acid to be            detected, which leads to the formation of a single stranded            nucleic acid,        -   hybridization of each of the strands of the nucleic acid            obtained during the previous denaturation step with at least            one primer according to the invention, by placing the            strands mentioned above with at least one primer couple            according to the invention under the conditions of            hybridization defined below,        -   formation, starting from the primers, of the DNA            complementary to the strands to which they are hybridized in            the presence of a polymerization agent (DNA polymerase) and            the four different nucleoside triphosphates (dNTP) which            leads to the formation of a greater number of            double-stranded nucleic acids to be detected than in the            previous denaturation step, this cycle being repeated a            defined number of times in order to obtain the said nucleic            acid sequence to be detected possibly present in the            biological sample in an amount sufficient to allow its            detection,    -   a step involving the detection of the possible presence of the        nucleic acid belonging to the genome of the virus of the HIV-1        and/or HIV-2 and/or SIV type in the biological sample.

The hybridization step described above is advantageously performed at60° C. for 1 minute 30 seconds in the “10× buffer”, the composition ofwhich (expressed as final concentrations for use) is indicated below.

The method of in vitro diagnosis of the invention may be carried outeither starting from the viral RNA, or from the episomal or integratedcomplementary DNA.

In fact, the genomes of the HIV and SIV viruses exist in the form of RNAor DNA, depending on the localization of the virus in the organism.

When the virus is situated within the cells of the organism, inparticular in the interior of blood cells, its RNA is recopied into DNAby a reverse transcriptase. On the other hand, the genome of the virusesof the HIV type in the extracellular medium, in particular in the blood,remains in the RNA form.

The extraction step according to the invention of the viral DNAcontained in the cells of the biological sample recommended by theinventors—in addition to the standard method usingphenol/chloroform—comprises the following steps:

-   -   suspension of the cell pellet in 0.5 ml of boiled water in a        Potter homogenizer with a wide pestle,    -   grinding of the cells by “forwards and backwards rotation”,    -   addition of Triton X100 to give a final concentration of 0.1%,    -   heat denaturation for 15 to 25 minutes at 100° C.,    -   brief centrifugation in order to remove only the cell debris,    -   precipitation of the DNA overnight at −20° C. by addition of 2.5        volumes of absolute ethanol and 10% of the final volume of 3        molar sodium acetate. The DNA is subsequently recovered, then        resuspended in boiled water after having been washed twice with        70° ethanol. It should be noted that this method leads to the        simultaneous precipitation of the DNAs and the RNAs which make        possible the detection of the genomic message of the viruses of        the HIV or SIV types by use of the method called “direct        PCR-DNA” or by that called “PCR-RNA”.

The step involving the extraction of the viral RNA is usually performedin the classical manner well-known to the person skilled in the art.

After extraction of the RNA, it is necessary to carry out an additionalstep involving the transformation of the single-stranded RNA intodouble-stranded DNA when the in vitro diagnosis of the invention isperformed on biological samples containing the viruses of the HIV-1and/or HIV-2 and/or SIV types, the genomes of which are in the RNA form.

This transformation of the RNA into DNA is carried out by treatment ofthe RNA obtained after extraction of the biological sample, inparticular serum, with a reverse transcriptase in a suitable medium.

The object of the invention more particularly among other things is amethod of in vitro diagnosis such as that defined above in which thestep of retrotranscription of viral RNA is carried out in the followingmanner:

-   -   10 μg of RNA, extracted and resuspended in water, is placed in        the presence of the primer couple at a concentration of 40 μM of        each in a final volume of 40 μl. The mixture is denatured at        100° C. for 10 minutes, then plunged into ice-cold water,    -   10 μl of the following mixture are added: 5 μl of the “10×        buffer” described below+1 unit of AMV (Avian Myeloblastosis        Virus) or MuMLV (Moloney Leukemia Virus) reverse transcriptase+1        unit of Taq-polymerase+1 μl of a 25 mM mixture of each of the 4        dNTP+water as required to give 10 μl. The final volume is thus        50 μl.

This reaction is carried out in two steps:

-   -   a) 1st step: synthesis of the cDNA by the action of the reverse        transcriptase at 42° C. for 13 minutes,    -   b) 2nd step: standard gene amplification: the mixture is heated        at 95° C. for 3 minutes to destroy the reverse transcriptase and        to carry out the dehybridization/hybridization step, then the        cycle previously described for gene amplification is initiated.

The object of the invention is more particularly a method of in vitrodiagnosis such as that described above in which the denaturation step isperformed in the presence of one or several primer couples of theinvention. In fact, as has been specified above, one of thecharacteristics of the oligonucleotides (or primers) of the invention isthat they give a clear-cut amplification band, usually free of aspecificbands, when they are used under the following conditions:

-   -   hybridization: the primers (1 μl of a 40 μmolar (40 μM) solution        of each primer) are placed in the presence of the matrix DNA        (100 to 300 ng) for the first step of        denaturation-reassociation; the tubes containing this mixture of        matrix DNA and primers is heated for 10 minutes at 100° C., then        plunged into ice-cold water in order to increase the extent of        matrix DNA/primer reassociation. The primers must be used at a        final concentration of 0.8 μM each in the amplification step        which follows.    -   amplification: the 4 dNTPs are added to the preceding mixture,        each being used at a concentration of 0.5 μmolar in the final        solution (50 μl), and one unit of Taq-polymerase per 50 μl of        reaction mixture; this step is carried out in an amplification        buffer of the present invention, usually designated by the name        “10× buffer”, the composition of which (when it is diluted 1/10)        is the following: Tris-HCl, pH 8.9: 50 mM; (NH₄)₂SO₄: 15 mM;        MgCl₂: 5 mM; β-mercaptoethanol: 10 mM; gelatin: 0.25 mg/ml. 5 μl        of this buffer and water to give 50 μl are added to the        preceding mixture.

The amplification cycles are performed in the following manner: 30 to 40cycles consisting of:

-   -   94° C. for 10 seconds (denaturation),    -   60° C. for 1 minute 30 (hybridization),    -   78° C. for 1 minute 30 (elongation).

The whole series is followed by a single cycle at 78° C. for 15 minutes.

The accuracy to ±0.3° C. of the temperatures indicated as well as theirstability during the different parts of the cycles, are essentialconditions for the production of maximal yields as well as insuring theabsence of aspecific bands.

The optimal concentration of DNA is 100 to 300 ng in the case of genomicDNA extracted from cells (of patients or in culture, mammals or otherspecies).

It is obvious that the preceding conditions represent optimal conditionsfor a final reaction mixture of 50 μl, and that these conditions may bemodified, depending on the final volume of the reaction mixture.

The use of several different primer couples (or cocktails of couples) ofthe invention makes possible either the cross-detection of several typesof the viruses of the HIV and/or SIV type, or the simultaneous detectionof several genes of a given virus of the HIV and/or SIV type.

As examples of the preferred primer couples which can be used within theframework of the present invention, mention may be made of the followingprimer couples:

-   -   MMy1-MMy4, MMy2-MMy4, MMy1-MMy3, MMy18-MMy19, MMy4a-MMy28a,        MMy28-MMy29a, MMy29-MMy30a, MMy31-MMy32a, in particular for the        in vitro diagnosis of the infection of an individual by HIV-1        and/or HIV-2    -   MMy5-MMy8, MMy6-MMy8, MMy7-MMy8, MMy5-MMy7a, MMy6-MMy7a,        MMy9-MMy11, MMy10-MMy11, MMy9-MMy10a, MMy26-MMy5a, MMy8a-MMy9a,        MMy8a-MMy89, MMy89a-MMy9a, MMy5-MMy17, MMy15-MMy16a,        MMy16-MMy17, MMy25-MMy27, MMy26-MMy27, in particular for the in        vitro diagnosis of the infection of an individual by HIV-1,    -   MMy20-MMy22, MMy20-MMy21a, MMy21-MMy22, MMy23-MMy24,        MMy12-MMy14, MMy12-MMy13a, for the in vitro diagnosis of the        infection of an individual by HIV-2.

The agent of polymerization used in the elongation step of the cycle isa thermostable DNA polymerase, in particular Taq polymerase, theamplifiose of the Appligene company or any thermostable DNA polymerasewhich is commercially available.

Generally speaking, the cycle of the method of in vitro diagnosis of theinvention is repeated between 30 and 40 times.

Depending on the nucleotide primer couples used, the method of in vitrodiagnosis of the invention also makes it possible to detect selectivelythe genes of the viruses of the HIV and/or SIV type present in thebiological sample.

As examples of the primer couples which can be used for theabove-mentioned method of diagnosis gene-per-gene of the invention arethe following:

-   -   MMy1-MMy4, MMy2-MMy4, MMy1-MMy3, MMy4a-MMy28a for the gag gene,    -   MMy18-MMy19 for the vpr gene,    -   MMy5-MMy8, MMy6-MMy8, MMy7-MMy8, MMy5-MMy7a, MMy6-MMy7a,        MMy26-MMy5a, MMy8a-MMy9a, MMy8a-MMy89, MMy89a-MMy9a for the env        gene,    -   MMy9-MMy11, MMy9-MMy10a, MMy10-MMy11 for the nef1 gene,    -   MMy15-MMy17, MMy15-MMy16a, MMy16-MMy17 for the vif1 gene,    -   MMy20-MMy22, MMy20-MMy21a, MMy21-MMy22 for the vif 2 gene,    -   MMy23-MMy24 for the vpx gene,    -   MMy12-MMy14, MMy12-MMy13a, MMy13-MMy14 for the nef2 gene,    -   MMy25-MMy27, MMy26-MMy27 for the vpu gene,    -   MMy28-MMy29a, MMy29-MMy30a, MMy30-MMy31a, MMy31-MMy32a for the        pol gene.

However, the combinations between “S” and “AS” primers described aboveare not limiting and may be varied according to the wish of the user.

The sizes of the nucleotide fragments synthesized with the aid of theprimer couples mentioned above as examples are shown in the followingTables I to XI:

(the figures indicated in the Tables below represent the number ofnucleotides in the fragments synthesized, and the “dashes” indicate thatthe primer couples tested do not make it possible to characterize thecorresponding viral strains).

TABLE I gag gag MMy1- MMy1- MMy2- MMy4a- MMy3 MMy4 MMy4 MMy28a HIV1-BRU265 750 532 671 HIV1-MAL 282 785 556 671 HIV1-ELI 265 750 538 674HIV2-ROD 354 845 544 663 SIV 343 844 544 668

TABLE II env env MMy5- MMy6- MMy7a MMy5-MMy8 MMy7a MMy6-MMy8 HIV1-BRU480 953 330 803 HIV1-MAL 471 944 321 794 HIV1-ELI 471 941 321 791HIV2-ROD — — — — SIV — — — —

TABLE III env env MMy7-MMy8 MMy26-MMy5a MMy8a-MMy9a HIV1-BRU 498 6911038 HIV1-MAL 498 691 1041 HIV1-ELI 495 679 1038 HIV2-ROD — — — SIV — ——

TABLE IV env env MMy8a-MMy89 MMy89a-MMy9a HIV1-BRU 411 646 HIV1-MAL 411649 HIV1-ELI 411 646 HIV2-ROD — — SIV — —

TABLE V nef1 nef1 MMy9-MMy10a MMy9-MMy11 MMy10-MMy11 HIV1-BRU 293 660388 HIV1-MAL 302 660 388 HIV1-ELI 296 663 388 HIV2-ROD — — — SIV — — —

TABLE VI nef2 nef2 MMy12-MMy13a MMy12-MMy14 MMy13-MMy14 HIV1-BRU — — —HIV1-MAL — — — HIV1-ELI — — — HIV2-ROD 400 792 415 SIV 400 755 378

TABLE VII vif1 vif1 MMy15-MMy16a MMy15-MMy17 MMy16-MMy17 HIV1-BRU 333603 293 HIV1-MAL 333 603 293 HIV1-ELI 333 603 293 HIV2-ROD — — — SIV — ——

TABLE VIII vpr vif2 MMy18-MMy19 MMy20-MMy21a MMy20-MMy22 HIV1-BRU 281 —— HIV1-MAL 281 — — HIV1-ELI 281 — — HIV2-ROD 319 352 659 SIV 308 352 656

TABLE IX vif2 vpx MMy21-MMy22 MMy23-MMy24 HIV1-BRU — — HIV1-MAL — —HIV1-ELI — — HIV2-ROD 329 329 SIV 326 329

TABLE X vpu pol MMy25-MMy27 MMy26-MMy27 MMy28-MMy29a HIV1-BRU 263 104623 HIV1-MAL 263 101 584 HIV1-ELI 263 101 584 HIV2-ROD — — 666 SIV — —712

TABLE XI pol pol MMy29- MMy30- MMy31- MMy30a MMy31a MMy32a HIV1-BRU 742869 826 HIV1-MAL 742 869 826 HIV1-ELI 742 869 826 HIV2-ROD 742 866 826SIV 742 866 826

It is to be noted that owing to their arrangement on the genome, theprimers used for amplification may be combined in a manner such thatthey can be used as probes, either after labelling with ³²P by means ofa kinase, or for use in the procedure employing cold probes to check thespecificity of the amplification band observed during an analysis by“Southern blot”. In addition to the classical combination of the primersin order that a third oligonucleotide may serve as specific internalprobe, the special case of the vif1/vpr and vif2/vpx genes due to theoverlapping of these genes, which permits cross-detection, is to benoted. Furthermore, during an analysis of the amplified DNA bysequencing, these oligonucleotides may be used as specific primes forthe DNA polymerase making possible a duplicate sequencing in each sense,hence a duplicate reading of the sequences, thus removing possibleambiguities in interpretation.

The object of the invention is also the primers such as those definedabove, labelled in particular radioactively or enzymatically, as well astheir use as nucleotide probes, in particular in the framework of themethod of in vitro diagnosis such as described above.

The object of the invention is also oligonucleotides such as thosedescribed above and containing sugars in the α-conformation. Sucholigonucleotides exhibit the property of reversing the sense of thedouble helix formed with the matrix (strand of the genome of the virus),this double helix thus passing from the “S” state to the “AS” state.

The invention also relates to the oligonucleotides described above inwhich some nucleotides are methylated and/or contain one or more sulfuratoms, in particular at the adenine residues. Such oligonucleotidespossess the property of increasing the stability of the double helix andconsequently of hybridizing better with the DNA strand to be amplified.

The invention also relates to the oligonuceotides such as thosedescribed above existing in the so-called “modified base” formcontaining nucleotides to which chromophores are covalently grafted(planar aromatic molecules such as acridine orange), in particularaccording to the method described in the article by C. Hélène publishedin “la Vie des Sciences”, compte-rendus, série générale, tome 4, No. 1,p. 17-37. Such oligonucleotides possess the property of being easilydetectable, in particular by fluorescence.

The oligonucleotides of the invention can also be used for theimplementation of a method of in vitro diagnosis of the infection ofmonkeys (macaque, mangabey monkey or green monkey) by the virus of theSIV type, this method duplicating the principal characteristics of thatdescribed above.

The object of the invention is also diagnostic kits for theimplementation of the methods of in vitro diagnosis mentioned above. Asan example, a diagnostic kit of the present invention contains:

-   -   at least one oligonucleotide primer couple according to the        invention, each couple consisting of a primer which hybridizes        with one of the strands of the nucleic acid sequence to be        detected, and a primer which hybridizes with the complementary        strand of this latter under the conditions defined above,    -   suitable reagents for the implementation of the cycle of        amplification operations, in particular a DNA polymerase and the        four different nucleoside triphosphates, and the reaction medium        designated “10× buffer” described above.    -   one (or more) probe which can be labelled, in particular by        radioactivity, and which is capable of hybridizing specifically        in the labelled or unlabelled form with the amplified nucleic        acid sequence(s) to be detected.

The invention also relates to the use of the primers of the inventionindicated above for the implementation of a procedure for the synthesisof proteins encoded in the nucleotide sequences amplified by means ofthese primers.

As an illustration, this procedure for the synthesis of proteinscomprises the amplification of the nucleotide sequences of the genomesof the viruses of the HIV or SIV type (coding for a specific proteinand, where appropriate, having undergone certain modifications of theirnucleotides) by placing in contact the said sequences with at least oneprimer couple according to the invention under the conditions describedabove, followed by the translation of these sequences thus amplifiedinto proteins; this last step is carried out in particular bytransformation of suitable host cells with the aid of vectors containingthe said amplified sequences, and the recovery of the proteins producedin these host cells.

The invention also relates to the polypeptides derived from thetranslation of the nucleotide sequences (or primers) of the invention.

The object of the invention is also the use of the anti-senseoligonucleotide primers as antiviral agents in general, in particular tocombat AIDS, as well as pharmaceutical compositions containing theseanti-sense primers in combination with a pharmaceutically acceptablevehicle.

The invention also relates to the immunogenic compositions containingone or more translation products of the nucleotide sequences accordingto the invention, and/or one or more translation products of thenucleotide sequences amplified according to the procedures describedabove starting from primers defined according to the invention, thesetranslation products being combined with a pharmaceutically acceptablevehicle.

The invention relates to the antibodies directed against one or more ofthe translation products described above (or, in other terms, capable ofgiving rise to an immunological reaction with one or more translationproducts of the nucleotide sequences according to the invention, or alsoone or more translation products of the amplified nucleotide sequencesstarting from primers defined according to the invention) and their usefor the implementation of methods of in vitro diagnosis of the infectionof an individual by a virus of the HIV-1 and/or HIV-2 type, or of ananimal by at least one of the three viruses (HIV-1, HIV-2, SIV)according to the procedures well-known to the person skilled in the art.

As an illustration, such a method of in vitro diagnosis according to theinvention comprises the placing in contact of a biological sample (inparticular serum), taken from a patient under study, with antibodiesaccording to the invention, and the detection by means of anyappropriate procedure (in particular with the aid of labelledanti-immunoglobulins) of the immunological complexes formed between theantigens of the viruses of the HIV or SIV type possibly present in thebiological sample and the said antibodies.

The object of the invention is also kits for in vitro diagnosiscontaining antibodies according to the invention and, where appropriate,suitable reagents for the detection of the immunological complex formedby reaction between the said antibodies and the antigens of the HIV orSIV viruses.

The invention also relates to a procedure for the preparation of thepolypeptides mentioned above, in particular those correspondingaccording to the universal genetic code to the nucleotide sequences (orprimers) described above, this procedure being characterized in that,starting preferably from the C-terminal amino acid, successive aminoacid residues are condensed successively one at a time in the requiredorder, or amino acid residues and fragments previously formed andalready containing several amino acid residues in the required order arecondensed, or also several fragments thus prepared beforehand arecondensed, it being understood that care will be taken to protectbeforehand all of the reactive functions borne by these amino acidresidues or fragments with the exception of the amine function of theone and the carboxyl function of the other, which normally mustparticipate in the formation of the peptide bonds, in particular afteractivation of the carboxyl function according to the known methods ofpeptide synthesis and this is continued in a stepwise manner until theN-terminal amino acid is reached.

For example, recourse may be had to the procedure of peptide synthesisin homogeneous solution described by Houbenweyl in “Methoden derOrganischen Chemie” (Methods of Organic Chemistry) edited by W. Wunsch,vol. 15-I and II, THIEME, STUTTGART, 1974, or to that of peptidesynthesis on a solid phase described by R. D. Merrifield in “Solid PhasePeptide Synthesis” (J. Am. Chem. Soc., 45, 2149-2154).

The invention also relates to a procedure for the preparation of thenucleotide sequences (or primers) described above, this procedurecomprising the following steps:

-   -   incubation of the genomic DNA, isolated from one of the viruses        of the HIV or SIV type mentioned above, with DNAase I, then        addition of EDTA and purification by extraction with the mixture        phenol/chloroform/isoamyl alcohol (25/24/1), then by ether,    -   treatment of the DNA thus extracted by Eco R1 methylase in the        presence of DTT, and purification by extraction as described        above,    -   incubation of the DNA thus purified with the 4 deoxynucleoside        triphosphates DATP, dCrP, dGTP and dTTP in the presence of T4        DNA polymerase and DNA ligase of E. coli, then purification        according to the method described above,    -   the cloning of the nucleic acid thus obtained in a suitable        vector and the recovery of the desired nucleic acid with the aid        of a suitable probe.

A particularly useful procedure for the preparation of the nucleotidesequences of the invention comprises the following steps:

-   -   the synthesis of DNA by using the β-cyanoethyl phosphoramidite        automated method described in Bioorganic Chemistry 4, 274-325        (1986),    -   the cloning of the nucleic acid thus obtained in a suitable        vector and the recovery of the nucleic acid by hybridization        with a suitable probe.

Another procedure for the preparation of the nucleotide sequences of theinvention comprises the following steps:

-   -   the set of chemically synthesized oligonucleotides, provided        with various restriction sites at their ends, the sequences of        which are compatible with the sequence of amino acids of the        natural polypeptide according to the principle described in        Proc. Natl. Acad. Sci. USA, 80, 7461-7465 (1983),    -   the cloning of the nucleic acid thus obtained in a suitable        vector and the recovery of the desired nucleic acid by        hybridization with a suitable probe.

1. A pol nucleic acid product produced by the process comprising: (a)providing a sample comprising a pol gene of HIV-1, HIV-2, or SIV nucleicacid; and (b) amplifying a template comprising sequence of the pol geneof the HIV-1, HIV-2, or SIV nucleic acid from the sample using a pair ofpurified polynucleotide primers chosen from: (1) a sense primer fromgroup (i) and an antisense primer from group (ii); wherein group (i)comprises nucleotides that hybridize to the nucleic acid, wherein thehybridizing nucleotides are chosen from 2021-2039, 2620-2643, 3339-3361,and 4186-4207 of the pol gene of HIV-1 Bru; and wherein group (ii)comprises nucleotides that hybridize to the nucleic acid, wherein thehybridizing nucleotides are chosen from 2643-2620, 3361-3339, 4207-4186,and 5011-4992 of a nucleic acid sequence complementary to the pol geneof HIV-1 Bru; (2) a sense primer from group (iii) and an antisenseprimer from group (iv); wherein group (iii) comprises nucleotides thathybridize to the nucleic acid, wherein the hybridizing nucleotides arechosen from 2055-2073, 2615-2638, 3333-3356, 4181-4202, and 4987-5006 ofthe pol gene of HIV-1 Mal; wherein group (iv) comprises nucleotides thathybridize to the nucleic acid, wherein the hybridizing nucleotides arechosen from 2073-2055, 2638-2615, 3356-3334, 4202-4181, and 5006-4987 ofa nucleic acid sequence complementary to the pol gene of HIV-1 Mal; (3)a sense primer from group (v) and an antisense primer from group (vi);wherein group (v) comprises nucleotides that hybridize to the nucleicacid, wherein the hybridizing nucleotides are chosen from 2024-2042,2584-2607, 3303-3325, 4150-4171, and 4956-4975 of the pol gene of HIV-1Eli; wherein group (vi) comprises nucleotides that hybridize to thenucleic acid, wherein the hybridizing nucleotides are chosen from2042-2024, 2607-2584, 3325-3303, 4171-4150, and 4975-4956 of a nucleicacid sequence complementary to the pol gene of HIV-1 Eli; (4) a senseprimer from group (vii) and an antisense primer from group (viii);wherein group (vii) comprises nucleotides that hybridize to the nucleicacid, wherein the hybridizing nucleotides are chosen from 2329-2349,2971-2994, 3690-3712, 4534-4555, and 5340-5359 of the pol gene of HIV-2ROD; wherein group (viii) comprises nucleotides that hybridize to thenucleic acid, wherein the hybridizing nucleotides are chosen from2349-2329, 2994-2971, 3712-3690, 4555-4534, and 5359-5340 of a nucleicacid sequence complementary to the pol gene of HIV-2 ROD; and (5) asense primer from group (ix) and an antisense primer from group (x)wherein group (ix) comprises nucleotides that hybridize to the nucleicacid, wherein the hybridizing nucleotides are chosen from 2299-2318,2887-3010, 3606-3628, 4450-4471, and 5256-5275 of the pol gene ofSIV-MAC; wherein group (x) comprises nucleotides that hybridize to thenucleic acid, wherein the hybridizing nucleotides are chosen from2318-2299, 3010-2887, 3628-3606, 4471-4450, and 5275-5256 of a nucleicacid sequence complementary to the pol gene of SIV-MAC; wherein theamplification is carried out under conditions that result in specificamplification of the pol nucleic acid product from HIV-1,HIV-2, or SIVnucleic acid.
 2. The nucleic acid product of claim 1, wherein theamplification is carried out in the presence of dNTPs, Taq-polymerase,and an amplification buffer comprising 50 mM of Tris-HCl, pH 8.9, 15 mM(NH₄)SO₄, 5 mM MgCl₂, 10 mM β-mercaptoethanol, 0.25 mg/ml gelatin, forfrom 30 to 40 cycles of 94° C. for 10 seconds, 60° C. for 1 minute and30 seconds, and 78° C. for 1 minute and 30 seconds; followed by a singlecycle at 78° C. for 15 minutes.
 3. The method of claim 1, wherein thepolynucleotide primers are linked to a promoter at the 5′ end.
 4. Themethod of claim 1, wherein the polynucleotide primers are from about 15nucleotides to about 30 nucleotides in length.
 5. The method of claim 1,wherein at least one of the polynucleotide primers is 27 nucleotides inlength.
 6. The method of claim 1, wherein at least one of thepolynucleotide primers is 40 nucleotides in length.
 7. The method ofclaim 1, wherein the polynucleotide primers are from 19 to 27nucleotides in length.
 8. The method of claim 1, wherein thepolynucleotide primers are from 19 to 24 nucleotides in length.
 9. Themethod of claim 1, wherein at least one of the polynucleotide primers is19 nucleotides in length.
 10. The method of claim 1, wherein at leastone of the polynucleotide primers is 24 nucleotides in length.
 11. A polnucleic acid product produced by the process comprising: (a) providing asample comprising a pol gene of HIV-1,HIV-2, or SIV nucleic acid; and(b) amplifying a template comprising sequence of the pol gene of theHIV-1,HIV-2, or SIV nucleic acid from the sample using a pair ofpurified polynucleotide primers chosen from: (1) a sense primer fromgroup (i) and an antisense primer from group (ii); wherein the 3′ end ofthe polynucleotides of group (i) consists of nucleotides 2021-2039,2620-2643, 3339-3361, or 4186-4207 of the pol gene of HIV-1 Bru; andwherein the 3′ end of the polynucleotides of group (ii) consists ofnucleotides 2643-2620, 3361-3339, 4207-4186, or 5011-4992 of a nucleicacid sequence complementary to the pol gene of HIV-1 Bru; (2) a senseprimer from group (iii) and an antisense primer from group (iv); whereinthe 3′ end of the polynucleotides of group (iii) consists of nucleotides2055-2073, 2615-2638, 3333-3356, 4181-4202, or 4987-5006 of the pol geneof HIV-1 Mal; and wherein the 3′ end of the polynucleotides of group(iv) consists of nucleotides 2073-2055, 2638-2615, 3356-3334, 4202-4181,or 5006-4987 of a nucleic acid sequence complementary to the pol gene ofHIV-1 Mal; (3) a sense primer from group (v) and an antisense primerfrom group (vi); wherein the 3′ end of the polynucleotides of group (v)consists of nucleotides 2024-2042, 2584-2607, 3303-3325, 4150-4171, or4956-4975 of the pol gene of HIV-1 Eli; and wherein the 3′ end of thepolynucleotides of group (vi) consists of nucleotides 2042-2024,2607-2584, 3325-3303, 4171-4150, or 4975-4956 of a nucleic acid sequencecomplementary to the pol gene of HIV-1 Eli; (4) a sense primer fromgroup (vii) and an antisense primer from group (viii); wherein the 3′end of the polynucleotides of group (vii) consists of nucleotides2329-2349, 2971-2994, 3690-3712, 4534-4555, and 5340-5359 of the polgene of HIV-2 ROD; and wherein the 3′ end of the polynucleotides ofgroup (viii) consists of nucleotides 2349-2329, 2994-2971, 3712-3690,4555-4534, or 5359-5340 of a nucleic acid sequence complementary to thepol gene of HIV-2 ROD; and (5) a sense primer from group (ix) and anantisense primer from group (x) wherein the 3′ end of thepolynucleotides of group (ix) consist of nucleotides 2299-2318,2887-3010, 3606-3628, 4450-4471, or 5256-5275 of the pol gene ofSIV-MAC; wherein the 3′ end of the polynucleotides of group (x) consistof nucleotides 2318-2299, 3010-2887, 3628-3606, 4471-4450, or 5275-5256of a nucleic acid sequence complementary to the pol gene of SIV-MAC;wherein the amplification is carried out under conditions that result inspecific amplification of the pol nucleic acid product from HIV-1,HIV-2,or SIV nucleic acid.
 12. The nucleic acid product of claim 11, whereinthe amplification is carried out in the presence of dNTPs,Taq-polymerase, and an amplification buffer comprising 50 mM ofTris-HCl, pH 8.9, 15 mM (NH₄)SO₄, 5 mM MgCl₂, 10 mM β-mercaptoethanol,0.25 mg/ml gelatin, for from 30 to 40 cycles of 94° C. for 10 seconds,60° C. for 1 minute and 30 seconds, and 78° C. for 1 minute and 30seconds; followed by a single cycle at 78° C. for 15 minutes.
 13. Themethod of claim 11, wherein the polynucleotide primers are linked to apromoter at the 5′ end.
 14. The method of claim 11, wherein thepolynucleotide primers are from about 15 nucleotides to about 30nucleotides in length.
 15. The method of claim 11, wherein at least oneof the polynucleotide primers is 27 nucleotides in length.
 16. Themethod of claim 11, wherein at least one of the polynucleotide primersis 40 nucleotides in length.
 17. The method of claim 11, wherein thepolynucleotide primers are from 19 to 27 nucleotides in length.
 18. Themethod of claim 11, wherein the polynucleotide primers are from 19 to 24nucleotides in length.
 19. The method of claim 11, wherein at least oneof the polynucleotide primers is 19 nucleotides in length.
 20. Themethod of claim 11, wherein at least one of the polynucleotide primersis 24 nucleotides in length.